Catalytic proteins-Enzymes

After reading this chapter you should be able to:

• General Characteristics of Enzymes

• Factors Affecting EnzymeActivity
• Enzyme Structure
• Enzyme classification
• Enzyme Specificity
• Medical Uses of Enzymes
• Enzyme Inhibition
• Regulation of Enzyme Activity
 Enzyme and activation energy

Definition:
Enzymes are mainly proteins that
catalyze chemical reactions under
physiological conditions. (Ribozymes
are catalytic RNA)

Enzymes accelerate the reaction rate,

by decreasing the activation energy of
the reaction
 Factors affecting the enzyme activity
Effect of temperature
In our body, enzymes function at temperature 37°C.

In an in-vitro context, Temperature, enzyme activity (until denaturation)

Effect of pH
Each enzyme have its optimum pH

ENZYME Optimum pH
Cytosolic 7-8
Pepsin (in gastric juice) 1.5-2
Trypsin, Chymotrypsin Alkaline (pancreatic juice)
Lysosomal enzymes Acidic

Various
Solutes: substrates, products, metal ions and regulatory molecules
 Definition of Enzyme Activity
Enzymatic activity depends on: Enzyme
1. Temperature
2. pH Substrate Product
3. Buffer
4. Substrate concentration and Coenzyme

Rate or velocity (v) of an enzymatic reaction= rate of conversion of substrate to product

per unit of time.
International unit (IU) for an enzyme = amount of enzyme that catalyzes conversion of
one micromole of substrate to product per min
1 IU = 1 μmol/min.
(katal ; 1 kat = 1 mol/s)

Specific activity of enzyme:

 Depends on the amount of protein
 μmol/min/mg of protein or IU/mg of protein
 Enzyme Structure
• SIMPLE ENZYMES
Composed only of protein

• CONJUGATED ENZYMES
Composed of:
– Apoenzyme
• Conjugate enzyme
without its cofactor

• Protein part of a
conjugated enzyme
• The apoenzyme can’t catalyze its reaction
– Coenzyme (Cofactor) without its cofactor.
• Non-protein part of a – The combination of the apoenzyme with the cofactor
makes the conjugated enzyme functional.
conjugated enzyme
• Holoenzyme = apoenzyme + cofactor
– The biochemically active conjugated enzyme.
 Coenzymes and cofactors

Cofactors

ion
Organic
(Coenzyme)

Tightly bound Loosly bound Tightly bound Loosely bound

Metaloenzyme Metal activated Prostethic Co-substrat
enzyme
 Reaction specificity and substrate specificity

Catalytic site

1. AA sequence of the
catalytic site

Binding site

Active site: Substrate binding site and the enzyme catalytic site.
 Reaction specificity and substrate
specificity are determined by the
structure of the active site
Catalytic site

1. AA sequence of the
catalytic site
2. Substrate size,
structure, charges,
polarity, and
hydrophobicity

Binding site

Active site: Substrate binding site and the enzyme catalytic site.
 Enzyme classification
Enzyme classification
Class Reaction Enzymes
dehydrogenases,
1. Oxidoreductases Ared+Box→Aox+Bred
peroxidases

2. Transferases A—B+C→A+B—C hexokinase, transamin-ases

3. Hydrolases A—B+H2O→A—H+B—OH alkaline phosphatase, trypsin

carbonic anhydrase,
4. Lyases (synthases) A(XH)—B→A—X+B—H
dehydratases

triose phosphate isomerase,

5. Isomerases A ⇌ ISO—A
phosphoglucomutase

pyruvate carboxylase, DNA

6. Ligases (synthetases) A+B+ATP→A—B+ADP+Pi
ligases

Nomenclature of Enzyme: Usually enzyme names are ended with -ase

eg. Amylase, Collagenase… some exceptions eg. Trypsin, Pepsin.

Or by two words; first word: majority of time substrate. Second word: reaction type

Enzyme commission number: EC x.y.z.. The x represent the enzyme class

Example: EC 2.1.3 is an ezyme that belong to transferase class (2)
 Isozymes:
Are different enzymes, that catalyze same reaction with different
affinities, in different tissues.

ATP
Glucose Glucose-6 phosphate
ADP

The enzymes that catalyze the reaction in our tissues are:

1- Hexokinase present in all tissues

2- Glucokinase present in Liver and Pancreatic beta cells only

(lower affinity than Hexokinase)
 LDH Isozyme
homo or hetero tetramers composed of M and H protein subunits

H H
H ↑↑↑ M↓↓↓ LDH-1
H H

M M
M↓↓↓ H ↑↑↑ LDH-5
M M

LDH-1 (4H)—in the heart and in RBC (red blood cells)

LDH-2 (3H1M)—in the reticuloendothelial system
LDH-3 (2H2M)—in the lungs
LDH-4 (1H3M)—in the kidneys, placenta, and pancreas
LDH-5 (4M)—in the liver and striated muscle
 Clinical diagnostic
Not required